tutorials.yaml

name: Run tutorials

on:
  push:
  pull_request:

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: ${{ github.ref != 'refs/heads/master' }}

jobs:
  installer:
    runs-on: ubuntu-latest

    defaults:
      run:
        shell: bash -l {0}

    steps:
      - name: Free space
        # HACK fixes 'No space left on device'
        # see: https://github.com/orgs/community/discussions/25678#discussioncomment-5242449
        # NOTE we don't use those, we use conda for everything anyway
        run: rm -rf /opt/hostedtoolcache

      - name: Checkout repository
        uses: actions/checkout@v4
        with:
            sparse-checkout: |
                docs
                tests
            sparse-checkout-cone-mode: false
            lfs: false

      - name: Install conda environment dependencies
        uses: conda-incubator/setup-miniconda@v3
        with:
          miniforge-version: latest
          miniforge-variant: Miniforge3
          mamba-version: "*"
          use-mamba: true
          no-implicit-channels: true
          channels: conda-forge,bioconda
          channel-priority: strict
          activate-environment: JupyText
          auto-update-conda: true
          environment-file: tests/conda_tutorials_env.yaml

      - name: Setup Jupyter kernel
        run: |
          python -m ipykernel install --user

      - name: Run installation notebooks
        working-directory: ./docs
        run: ./convert.sh --branch *_install.md

      - name: Create V-pipe installation archive
        # HACK this acceleraters upload while preserving Unix-specifics (case sensitivity, file attributes).
        run: tar --zstd -cvf vpipeinstallation.tar.zst ./docs/vp-analysis

      - name: Keep installation
        uses: actions/upload-artifact@v4
        with:
          name: VPipeInstallation
          path: vpipeinstallation.tar.zst
          if-no-files-found: error

      - name: Save notebooks
        uses: actions/upload-artifact@v4
        with:
          name: JupyterNotebooks-Install
          path: ./docs/*.ipynb


  tutorial:
    needs: installer

    strategy:
      max-parallel: 5
      fail-fast: false
      matrix:
         virus: ["hiv", "sarscov2"]

    runs-on: ubuntu-latest

    defaults:
      run:
        shell: bash -l {0}

    steps:
      - name: Free space
        # HACK fixes 'No space left on device'
        # see: https://github.com/orgs/community/discussions/25678#discussioncomment-5242449
        # NOTE we don't use those, we use conda for everything anyway
        run: rm -rf /opt/hostedtoolcache

      - name: Checkout repository
        uses: actions/checkout@v4
        with:
            sparse-checkout: |
                docs
                tests
            sparse-checkout-cone-mode: false
            lfs: false

      - name: Reuse installation
        uses: actions/download-artifact@v4
        with:
            name: VPipeInstallation

      - name: Extract V-pipe installation archive
        run: tar --zstd -xvf vpipeinstallation.tar.zst

      - name: Install conda environment dependencies
        uses: conda-incubator/setup-miniconda@v3
        with:
          miniforge-version: latest
          miniforge-variant: Miniforge3
          python-version: "3.11"
          mamba-version: "*"
          use-mamba: true
          no-implicit-channels: true
          channels: conda-forge,bioconda
          channel-priority: strict
          activate-environment: JupyText
          auto-update-conda: true
          environment-file: tests/conda_tutorials_env.yaml

      - name: Setup Jupyter kernel
        run: |
          python -m ipykernel install --user

      - name: Run analysis notebooks
        working-directory: ./docs
        run: ./convert.sh --version --branch --sralog tutorial*_${{ matrix.virus }}.md

      - name: Save output
        if: ${{ failure() }}
        uses: actions/upload-artifact@v4
        with:
          name: Tutorial_${{ matrix.virus }}
          path: |
            ./docs/*.ipynb
            ./docs/*.log
            ./docs/samples/*
            ./docs/vp-analysis/work*
            !./docs/vp-analysis/work*/.snakemake/conda/*/
          include-hidden-files: true
          if-no-files-found: ignore

      - name: Save notebooks
        uses: actions/upload-artifact@v4
        with:
          name: JupyterNotebooks-${{ matrix.virus }}
          path: ./docs/*.ipynb

      # - name: Publish
      #   uses: peaceiris/actions-gh-pages@v3
      #   with:
      #     github_token: ${{ secrets.GITHUB_TOKEN }}
      #     publish_dir: ./docs